The DNA of higher animals carries a minor fraction of its cytosine in the modified form 5-methyl cytosine. There is reason to think that this modification of the genetic material itself, an activity that nature has usually avoided, must have a specific and important purpose when and where it does occur. Our goal is to relate cytosine modification to two important processes governing how the genome is used: 1) transcription and 2) gene rearrangement and/or amplification. 5-methyl cytosine-containing sequences can be identified using restriction endonucleases which are sensitive to methylation. By this means we have already located many repeated sequences in chicken DNA which show a concerted methylation pattern among hundreds or thousands of copies. Methylated and unmethylated prototype sequences are being isolated by molecular cloning. The cloned DNA segments are being used to measure transcription (RNA-DNA hybridization in solution, Northern blotting) and genome reorganization (Southern blotting of restricted genomic DNA). We are also sequencing cloned DNA segments to determine the context in which 5-methyl cytosine occurs.